RIOX1

ribosomal oxygenase 1, the group of Iron (II) and 2-oxoglutarate dependent oxygenases

Basic information

Region (hg38): 14:73490933-73493394

Previous symbols: [ "C14orf169" ]

Links

ENSG00000170468

∙ NCBI:79697 ∙ OMIM:611919 ∙ HGNC:20968 ∙ Uniprot:Q9H6W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIOX1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1 clinvar		1
missense			1 clinvar		1 clinvar	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	1

Variants in RIOX1

This is a list of pathogenic ClinVar variants found in the RIOX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
14-73491097-G-A	not specified	Uncertain significance (Aug 09, 2021)	3154479
14-73491111-C-A		Benign (Dec 31, 2019)	768664
14-73492604-C-G		Benign/Likely benign (Sep 01, 2022)	788892

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates 'Lys-4' (H3K4me) and 'Lys-36' (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' (H3K4me3) and monomethylated H3 'Lys-4' (H3K4me1) residues, while it has weaker activity for dimethylated H3 'Lys-36' (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on 'His-216'. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC- induced transcriptional activation. {ECO:0000250, ECO:0000269|PubMed:14742713, ECO:0000269|PubMed:17308053, ECO:0000269|PubMed:23103944}.;

Mouse Genome Informatics

Gene name: Riox1
Phenotype: skeleton phenotype; immune system phenotype; growth/size/body region phenotype; hematopoietic system phenotype; craniofacial phenotype; cellular phenotype;

Gene ontology

Biological process: histone H3-K4 demethylation;negative regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;oxidation-reduction process;histone H3-K36 demethylation
Cellular component: nucleus;nucleoplasm;nucleolus
Molecular function: iron ion binding;protein binding;2-oxoglutarate-dependent dioxygenase activity;histone demethylase activity (H3-K4 specific);histone demethylase activity (H3-K36 specific)